Thermal processing is common in semiconductor manufacturing. Semiconductor substrates are often subjected to thermal treatment following a material process such as deposition, implantation, or etching. Temperature of a substrate undergoing a thermal process is often measured. In some such processes, heat sources in the chamber produce a large amount of thermal energy that can overwhelm thermal energy being emitted by the substrate. Thus, there is a continuing need for methods and apparatus for measuring temperature of a substrate during thermal processing.